Mauricio Carneiro 80d92e0c63 Allowing the GATK to have non-required outputs ... Modified the SAMFileWriterArgumentTypeDescriptor to accept output bam files that are null if they're not required (in the @Output annotation). This change enables the nWayOut parameter for the IndeRealigner and ReduceReads to operate optionally while maintaining the original single way out. [#DEV-10 transition:31 resolution:1]		2012-10-15 13:49:08 -04:00
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datasources	ExperimentalReadShardBalancerUnitTest was being skipped; fixed	2012-09-22 01:56:39 -04:00
downsampling	Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"	2012-09-10 15:52:39 -04:00
executive	…
filters	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
iterators	Experimental, downsampler-friendly read shard balancer	2012-09-21 22:17:58 -04:00
refdata	Part I of GSA-462: Consistent RODBinding access across Ref and Read trackers	2012-08-30 10:15:10 -04:00
report	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
samples	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
traversals	Refactor TraversalEngine to extract the progress meter functions	2012-09-10 20:14:13 -04:00
walkers	Allowing the GATK to have non-required outputs	2012-10-15 13:49:08 -04:00
CommandLineGATKUnitTest.java	Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us.	2012-07-18 21:48:58 -04:00
EngineFeaturesIntegrationTest.java	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
GenomeAnalysisEngineUnitTest.java	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
WalkerManagerUnitTest.java	Fixing walker unit test with the new naming convention	2012-07-20 17:50:29 -04:00